[English] 日本語
Yorodumi- EMDB-11898: Tomographic reconstruction of native glycolipoprotein filaments i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11898 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tomographic reconstruction of native glycolipoprotein filaments in honeybee royal jelly | |||||||||
Map data | Tomographic reconstruction of native RJ filaments | |||||||||
Sample |
| |||||||||
Biological species | Apis mellifera (honey bee) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Mattei S / Ban A / Picenoni A / Leibundgut M / Glockshuber R / Boehringer D | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structure of native glycolipoprotein filaments in honeybee royal jelly. Authors: Simone Mattei / Arvid Ban / Armin Picenoni / Marc Leibundgut / Rudi Glockshuber / Daniel Boehringer / Abstract: Royal jelly (RJ) is produced by honeybees (Apis mellifera) as nutrition during larval development. The high viscosity of RJ originates from high concentrations of long lipoprotein filaments that ...Royal jelly (RJ) is produced by honeybees (Apis mellifera) as nutrition during larval development. The high viscosity of RJ originates from high concentrations of long lipoprotein filaments that include the glycosylated major royal jelly protein 1 (MRJP1), the small protein apisimin and insect lipids. Using cryo-electron microscopy we reveal the architecture and the composition of RJ filaments, in which the MRJP1 forms the outer shell of the assembly, surrounding stacked apisimin tetramers harbouring tightly packed lipids in the centre. The structural data rationalize the pH-dependent disassembly of RJ filaments in the gut of the larvae. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11898.map.gz | 13.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11898-v30.xml emd-11898.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_11898.png | 145.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11898 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11898 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_11898.map.gz / Format: CCP4 / Size: 40.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Tomographic reconstruction of native RJ filaments | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 11.096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Royal jelly glycolipoprotein filaments
Entire | Name: Royal jelly glycolipoprotein filaments |
---|---|
Components |
|
-Supramolecule #1: Royal jelly glycolipoprotein filaments
Supramolecule | Name: Royal jelly glycolipoprotein filaments / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Apis mellifera (honey bee) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 4 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: BBI / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 6.3 µm / Calibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-4 / Number grids imaged: 1 / Average exposure time: 1.6 sec. / Average electron dose: 2.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
---|---|
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41 |